bug#44613: closed ([PATCH] Fix build for bedtools)

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Your message dated Fri, 13 Nov 2020 15:00:57 +0100
with message-id <ae90892f71f1907efc846c45bba2d13fbf9a78ef.camel@gnu.org>
and subject line Re: [bug#44613] [PATCH] Fix build for bedtools
has caused the debbugs.gnu.org bug report #44613,
regarding [PATCH] Fix build for bedtools
to be marked as done.

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44613: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=44613
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--- Begin Message --- Subject: [PATCH] Fix build for bedtools Date: Fri, 13 Nov 2020 12:01:04 +0100 User-agent: Evolution 3.38.1 (3.38.1-1.fc33)

Dear Guix,

By updating samtools to 1.11, I introduced a build failure for
bedtools. More precisely, the tests for intersect break in precisely
this way:
https://github.com/arq5x/bedtools2/issues/814

With the following patches, I'd like to add samtools-1.9, htslib-1.9
(samtools depends on that) to fix this problem with bedtools.

Alternatively we could add a patch to disable the failing bedtools
tests.  I manually inspected the test results, and seem to match
perfectly (indicating that there's no problem with bedtools).

Kind regards,
Roel Janssen

0003-gnu-bedtools-Use-samtools-1.9.patch
Description: Text Data

0002-gnu-Add-samtools-1.9.patch
Description: Text Data

0001-gnu-Add-htslib-1.9.patch
Description: Text Data

--- End Message ---

> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#44613] [PATCH] Fix build for bedtools
>
>
>
>
> Date: 
>
> Fri, 13 Nov 2020 15:00:57 +0100
>
>
>
>
> User-agent: 
>
> Evolution 3.38.1 (3.38.1-1.fc33) 
>
>
>
>
> Hi Simon,
>
> On Fri, 2020-11-13 at 14:34 +0100, zimoun wrote:
> > Hi Roel,
> > 
> > On Fri, 13 Nov 2020 at 13:55, Roel Janssen <roel@gnu.org> wrote:
> > 
> > > I also tried removing the bundled htslib for bedtools, but didn't
> > > go
> > > this route for two reasons:
> > > - The bundled htslib for bedtools seems "slightly modified" (I
> > > didn't
> > > investigate further)
> > > - Replacing the references to libhts.a with $(pkg-config htslib --
> > > cflags --libs) produced various linker errors. So I stopped right
> > > there.
> > > 
> > > I'm sure more tools will likely have failed because of the htslib
> > > upgrade (sorry about this!), so having htslib-1.9 around for some
> > > time
> > > may be a good fallback for now.
> > 
> > Thank for your explanations.
> > 
> > 
> > > Just to double-check: Is it OK to push the proposed patches?
> > 
> > I have not tried them but they LGTM.
> > 
>
> Thanks for the quick review. I pushed the patches in
> c3232fcc7785abc1057a0d4b5b1832f1e39c9c1b,
> da4a38edad52f7bb5a8d41465d09f3f0197fd0b7, and
> 3ede804f6d4c38ff0b9a5705544a8c35f6827ff1.
>
> Kind regards,
> Roel Janssen
>
>
>
>
> --- End Message ---